Contacts of the strand formed by residues 138 - 143 (chain B) in PDB entry 4AOR
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLN 138 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B GLY 3.4 5.3 + - - +
137B THR* 1.3 82.4 - - - +
139B CYS* 1.3 60.5 + - - +
162B LYS* 3.8 35.0 - - + +
163B ALA 3.8 3.1 - - - +
164B PRO* 3.2 37.4 - - - +
188B TYR* 4.2 5.2 + - - -
206B CYS* 4.2 5.9 - - - -
207B SER 4.8 2.6 + - - -
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Residues in contact with CYS 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B THR* 4.0 2.9 - - - -
138B GLN* 1.3 76.2 - - - +
140B LEU* 1.3 60.7 + - - +
141B ILE* 4.9 2.6 - - + +
161B LEU 3.6 0.3 - - - +
162B LYS* 3.2 11.3 - - - +
163B ALA 2.8 36.3 + - - +
165B ILE* 3.8 24.2 - - - -
204B VAL* 3.7 17.7 - - + -
205B VAL 3.2 7.0 - - - +
206B CYS* 2.0 48.0 - - - -
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Residues in contact with LEU 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B TYR* 3.6 23.8 - - - +
34B THR 5.8 0.4 - - - +
35B VAL* 4.2 22.0 - - + -
37B TYR* 4.0 20.7 + - - +
139B CYS* 1.3 73.6 - - - +
141B ILE* 1.3 64.1 + - - +
142B SER* 5.1 2.1 + - - -
160B CYS* 3.8 17.7 - - + -
161B LEU 3.6 15.9 - - - +
162B LYS* 4.3 14.4 - - + +
203B PRO* 3.6 2.8 - - - +
204B VAL* 3.4 2.3 - - - -
205B VAL* 2.7 43.1 + - + +
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Residues in contact with ILE 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B ILE* 4.0 18.6 - - + +
139B CYS* 4.9 1.1 - - + +
140B LEU* 1.3 80.3 - - - +
142B SER* 1.3 65.0 + - - +
160B CYS* 3.4 3.8 - - - +
161B LEU* 2.8 43.8 + - + +
163B ALA* 3.9 28.3 - - + +
186B ALA* 4.8 4.9 - - + +
187B GLY* 6.0 0.2 - - - -
195B SER* 4.2 7.6 - - - -
203B PRO 3.4 11.4 - - - +
204B VAL* 4.0 19.5 - - + -
214B VAL* 3.9 21.3 - - + -
229B TYR* 3.6 28.3 - - + +
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Residues in contact with SER 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ILE* 4.0 8.4 - - - +
35B VAL* 3.6 16.3 - - - +
37B TYR* 5.1 0.5 + - - -
38B GLN* 2.8 29.5 + - - +
140B LEU* 5.1 2.7 + - - +
141B ILE* 1.3 81.4 - - - +
143B GLY* 1.3 58.3 + - - +
158B LEU* 4.4 4.9 - - - -
159B LYS 3.2 13.7 - - - -
160B CYS* 4.1 14.8 - - - -
199B ASP* 4.4 4.0 - - - +
202B GLY* 4.4 6.8 - - - -
203B PRO* 3.5 22.9 + - - +
214B VAL* 4.8 1.6 - - - +
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Residues in contact with GLY 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ILE* 3.7 3.2 - - - +
38B GLN* 4.1 8.7 - - - -
49B GLY* 6.2 1.1 - - - -
142B SER* 1.3 77.0 - - - +
144B TRP* 1.3 59.1 + - - -
145B GLY 3.4 0.6 + - - -
158B LEU* 3.5 15.3 - - - +
159B LYS* 3.0 36.1 + - - +
199B ASP* 3.2 18.4 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il